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Data Search and Retrieval

Explore different types of data including metadata, flat files, sequences, and analysis available from European Nucleotide Archive. Learn how to search and download data by accession, taxon, text, or sequence. Access ENA resources for efficient data retrieval.

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Data Search and Retrieval

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  1. Data Search and Retrieval European Nucleotide Archive Nicole Silvester www.ebi.ac.uk/ena

  2. Objectives • Understand the different types of data available from ENA • Know how to find/download them

  3. Data available from ENA • Metadata (XML or tab-separated text) • Flat files • Sequences (FASTA) • Raw reads (FASTQ or submitted format) • Analysis (submitted format)

  4. Searching for data • By accession • By taxon • By search conditions: • Text search • Advanced search • By sequence: • Sequence search

  5. Accession entry point • http://ebi.ac.uk/ena/data/view/<ACCESSION> • http://www.ebi.ac.uk/ena/data/view/ERS027401 • Retrieve XML format • http://www.ebi.ac.uk/ena/data/view/ERS027401&display=XML • Retrieve Flat file • http://www.ebi.ac.uk/ena/data/view/AF059042&display=TEXT • Retrieve FASTA sequence • http://www.ebi.ac.uk/ena/data/view/AF059042&display=FASTA

  6. Taxon entry point • NCBI tax ID • http://www.ebi.ac.uk/ena/data/view/Taxon:6643 • Scientific name • http://www.ebi.ac.uk/ena/data/view/Taxon:Octopus • Retrieve FASTA sequences • http://www.ebi.ac.uk/ena/data/view/Taxon:6643&subtree=true&portal=sequence_release&offset=1&length=1000&display=fasta&download=fasta

  7. Text Search vs Advanced Search • Text search: • “full text” search • terms searched against data files • searches across all ENA data domains • Advanced search: • “field-based” search • search against specific meta-data fields • searches within chosenENA data domain

  8. Text Search vs Advanced Search • want: human sequences

  9. Text Search vs Advanced Search • want: human mRNA sequences

  10. Sequence Search • http://www.ebi.ac.uk/ena/search/

  11. Resources • http://www.ebi.ac.uk/ena/about/browser • http://www.ebi.ac.uk/ena/about/marker-portal-web-interface • http://www.ebi.ac.uk/ena/about/taxon-portal-web-interface • http://www.ebi.ac.uk/ena/about/data_download • http://www.ebi.ac.uk/ena/about/sequence_download • http://www.ebi.ac.uk/ena/about/read_download • http://www.ebi.ac.uk/ena/about/sequence_search

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